Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for NCOA2
Basic gene info.Gene symbolNCOA2
Gene namenuclear receptor coactivator 2
SynonymsGRIP1|KAT13C|NCoA-2|SRC2|TIF2|bHLHe75
CytomapUCSC genome browser: 8q13.3
Genomic locationchr8 :71024266-71316020
Type of geneprotein-coding
RefGenesNM_006540.2,
Ensembl idENSG00000140396
Descriptionclass E basic helix-loop-helix protein 75glucocorticoid receptor-interacting protein-1hTIF2transcriptional intermediary factor 2
Modification date20141207
dbXrefs MIM : 601993
HGNC : HGNC
Ensembl : ENSG00000140396
HPRD : 09066
Vega : OTTHUMG00000164671
ProteinUniProt: Q15596
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NCOA2
BioGPS: 10499
Gene Expression Atlas: ENSG00000140396
The Human Protein Atlas: ENSG00000140396
PathwayNCI Pathway Interaction Database: NCOA2
KEGG: NCOA2
REACTOME: NCOA2
ConsensusPathDB
Pathway Commons: NCOA2
MetabolismMetaCyc: NCOA2
HUMANCyc: NCOA2
RegulationEnsembl's Regulation: ENSG00000140396
miRBase: chr8 :71,024,266-71,316,020
TargetScan: NM_006540
cisRED: ENSG00000140396
ContextiHOP: NCOA2
cancer metabolism search in PubMed: NCOA2
UCL Cancer Institute: NCOA2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NCOA2 in cancer cell metabolism1. Qin J, Lee H-J, Wu S-P, Lin S-C, Lanz RB, et al. (2014) Androgen deprivation–induced NCoA2 promotes metastatic and castration-resistant prostate cancer. The Journal of clinical investigation 124: 5013. go to article

Top
Phenotypic Information for NCOA2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NCOA2
Familial Cancer Database: NCOA2
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 601993; gene.
Orphanet
DiseaseKEGG Disease: NCOA2
MedGen: NCOA2 (Human Medical Genetics with Condition)
ClinVar: NCOA2
PhenotypeMGI: NCOA2 (International Mouse Phenotyping Consortium)
PhenomicDB: NCOA2

Mutations for NCOA2
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryNCOA2chr87107749971077519NCOA2chr87106125271061272
ovaryNCOA2chr87115636971156389NCOA2chr87115267971152699
ovaryNCOA2chr87126749171267511NCOA2chr87126895971268979
ovaryNCOA2chr87128140671281426NCOA2chr87129510071295120
pancreasNCOA2chr87107995471079974chr87747815677478176
pancreasNCOA2chr87108103071081050NCOA2chr87108131571081335
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NCOA2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
EF374064KAT6A17584179477441794848NCOA27547687105344171057084
AW979049NCOA29024387121859671218749SLC35B42414567133984283133986549
BG260721NCOA2129687126123071261525SLC7A1281418133008355130083688
AA829002NCOA2418887121856571218749NCOA218432687121844771218589
BG674032NCOA2115587117263571172788MAP2K3148723172121357421214148
AA829004NCOA2418887121856571218749NCOA218433087121844771218593
DA677327NCOA2112987131593571316063KLHL28129595144541435445415132
BG222207HMGN3710567992310279923200NCOA210625787129482671294977
BE009179NCOA21038087111039171110761PTPRE36444310129789785129789864
BF379189AKAP131235158595955285959789NCOA222736287124623271246367
BE149299THSD7B1601802137875796137875816NCOA216840987121844471218685
BF811949NCOA22331587109200071092293NCOA231046487109167171091825
BF088409NCOA2314287124643571246573RHOB14143622064863220648927
AL706656NCOA2234387129098171291001CAPZB2682611967217119672964

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample4  1  1 2 2  11  
GAIN (# sample)3  1  1 2 1  11  
LOSS (# sample)1         1      
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

Top
check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=4

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=134)
Stat. for Synonymous SNVs
(# total SNVs=34)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

Top
check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr8:71074996-71074996p.A309V3
chr8:71078928-71078928p.R201R3
chr8:71068854-71068854p.S582S2
chr8:71044133-71044133p.R1088Q2
chr8:71033568-71033568p.D1451G2
chr8:71087088-71087088p.A89V2
chr8:71068691-71068691p.G637W2
chr8:71068901-71068901p.V567F2
chr8:71082499-71082499p.Y160C2
chr8:71069094-71069094p.I502I2

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample341292 5 41 13921 1322 14
# mutation341282 5 41 16921 1630 20
nonsynonymous SNV32 231 3 2  15821 1322 13
synonymous SNV 2151 2 21 11   38 7
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

Top
check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr8:71074996p.A309V3
chr8:71068967p.G545W2
chr8:71039179p.P384L2
chr8:71037031p.L1206P2
chr8:71039182p.R1329L2
chr8:71044133p.P470P2
chr8:71069449p.R201R2
chr8:71040732p.R1088P2
chr8:71069190p.T1262N2
chr8:71078928p.R1261Q2

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for NCOA2 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

Top
Gene Expression for NCOA2

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

APOOL,ARFGEF1,ASXL2,CCNT1,CLOCK,DDI2,GTF2A1,
LMBRD2,NCOA2,RAPGEF6,REST,RSC1A1,SERINC5,TMED10P1,
UBR5,UHMK1,VCPIP1,VPS13B,YTHDF3,ZNF623,ZNF704
ARFGEF2,BIRC6,BPTF,CCNT1,CHD6,EP300,KDM5A,
LATS1,LMTK2,MGA,MYSM1,NCOA2,PDPK1,RAPGEF6,
REST,RSF1,SMCR8,UBR5,ZKSCAN1,ZKSCAN8,ZNF827

ARFGEF1,ASXL2,CCNT1,DDI2,EP300,FAM168A,GTF2A1,
HIPK3,LATS1,LCOR,MYO9A,NCOA2,RC3H2,REL,
REST,STRN,TAOK1,UBR5,VPS13B,ZNF623,ZNF827
ARHGEF12,ATXN7,BIRC6,CCDC93,EP300,FOXJ3,GBF1,
GOLGB1,HEATR5B,KDM5A,LCOR,MARCH6,MGAT5,MTMR3,
NCOA2,NCOA6,NF1,RALGAPB,SOS1,UBR4,ZFYVE26
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for NCOA2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2095163; -.
Organism-specific databasesPharmGKB PA31471; -.
Organism-specific databasesCTD 10499; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01645nuclear receptor coactivator 2experimentalGenistein
DB02998nuclear receptor coactivator 2experimentalMethyltrienolone
DB06871nuclear receptor coactivator 2experimental17-METHYL-17-ALPHA-DIHYDROEQUILENIN
DB06898nuclear receptor coactivator 2experimental4-(2-amino-1-methyl-1H-imidazo[4,5-b]pyridin-6-yl)phenol
DB07080nuclear receptor coactivator 2experimentalN-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE
DB07086nuclear receptor coactivator 2experimental4-[(1S,2S,5S)-5-(HYDROXYMETHYL)-8-METHYL-3-OXABICYCLO[3.3.1]NON-7-EN-2-YL]PHENOL
DB07087nuclear receptor coactivator 2experimental4-[(1S,2S,5S,9R)-5-(HYDROXYMETHYL)-8,9-DIMETHYL-3-OXABICYCLO[3.3.1]NON-7-EN-2-YL]PHENOL
DB07195nuclear receptor coactivator 2experimental4-[(1S,2S,5S)-5-(HYDROXYMETHYL)-6,8,9-TRIMETHYL-3-OXABICYCLO[3.3.1]NON-7-EN-2-YL]PHENOL
DB07678nuclear receptor coactivator 2experimental(9ALPHA,13BETA,17BETA)-2-[(1Z)-BUT-1-EN-1-YL]ESTRA-1,3,5(10)-TRIENE-3,17-DIOL
DB07707nuclear receptor coactivator 2experimental(9BETA,11ALPHA,13ALPHA,14BETA,17ALPHA)-11-(METHOXYMETHYL)ESTRA-1(10),2,4-TRIENE-3,17-DIOL
DB07708nuclear receptor coactivator 2experimental3-CHLORO-2-(4-HYDROXYPHENYL)-2H-INDAZOL-5-OL
DB07712nuclear receptor coactivator 2experimental3-ETHYL-2-(4-HYDROXYPHENYL)-2H-INDAZOL-5-OL
DB07863nuclear receptor coactivator 2experimental2-chloro-5-nitro-N-phenylbenzamide
DB07932nuclear receptor coactivator 2experimentaldimethyl (1R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxylate
DB08047nuclear receptor coactivator 2experimental4-[1-allyl-7-(trifluoromethyl)-1H-indazol-3-yl]benzene-1,3-diol
DB08048nuclear receptor coactivator 2experimental4-(6-HYDROXY-1H-INDAZOL-3-YL)BENZENE-1,3-DIOL
DB08175nuclear receptor coactivator 2experimental(2E,4E)-11-METHOXY-3,7,11-TRIMETHYLDODECA-2,4-DIENOIC ACID
DB08320nuclear receptor coactivator 2experimentalDIETHYL (1R,2S,3R,4S)-5,6-BIS(4-HYDROXYPHENYL)-7-OXABICYCLO[2.2.1]HEPT-5-ENE-2,3-DICARBOXYLATE
DB08398nuclear receptor coactivator 2experimental2-AMINO-1-METHYL-6-PHENYLIMIDAZO[4,5-B]PYRIDINE
DB08402nuclear receptor coactivator 2experimental2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID
DB08595nuclear receptor coactivator 2experimental4-[(1S,2R,5S)-4,4,8-TRIMETHYL-3-OXABICYCLO[3.3.1]NON-7-EN-2-YL]PHENOL
DB08601nuclear receptor coactivator 2experimentaltributylstannanyl
DB08773nuclear receptor coactivator 2experimentalRALOXIFENE CORE


Top
Cross referenced IDs for NCOA2
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas